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United States Department of Agriculture

Agricultural Research Service

Research Project: ENVIRONMENTALLY SOUND MANURE MANAGEMENT FOR REDUCTION OF GAS EMISSIONS, NUTRIENTS, AND PATHOGENS

Location: Agroecosystem Management Research

Title: Mining metagenomic datasets for antibiotic resistance genes

Author
item Durso, Lisa

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: January 21, 2013
Publication Date: January 23, 2013
Citation: Durso, L.M. 2013. Mining metagenomic datasets for antibiotic resistance genes. In: Nelson, K. editor. Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Berlin/Heidelberg, Germany: Springer-Verlag. DOI:10.1007/SpringerReference_332403 2013-01-23 22:12:18 UTC.

Interpretive Summary: Antibiotics are widely used to kill, slow down, or prevent the growth of susceptible bacteria. There are many different kinds of antibiotics, multiple mechanisms of resistance and dozens of genes that are involved in coding for antibiotic resistance. Antibiotic resistance is a normal and natural phenomenon that can be documented even in ancient samples and pristine habitats. In addition to naturally occurring antibiotic resistance, there is no doubt that human associated use of antibiotics s for health, food production, veterinary, and industrial purposes has dramatically impacted resistance. This chapter looks at using large datasets to answer questions regarding which antibiotic resistance genes are present in any particular sample, and which bacteria are likely carrying those genes. Knowing which genes are present is one step to learning about antibiotic resistance, and needs to be combined with information about how the bacteria live in the wild.

Technical Abstract: Antibiotics are medicines that are used to kill, slow down, or prevent the growth of susceptible bacteria. They became widely used in the mid 20th century for controlling disease in humans, animals, and plants, and for a variety of industrial purposes. Antibiotic resistance is a broad term. There are many different kinds of antibiotics, multiple mechanisms of resistance and dozens of genes that are involved in coding for antibiotic resistance. Antibiotic resistance is a normal and natural phenomenon that can be documented even in ancient samples and pristine habitats. In addition to naturally occurring antibiotic resistance, there is no doubt that anthropogenic, or human associated use of antibiotics s for health, food production, veterinary, and industrial purposes has dramatically impacted resistance. The term “metagenomic” has multiple meanings. Historically it was used to describe the kind of sample that was collected, and referred to collecting DNA or genomic information not just from a single organism or isolate, but from a whole community, a meta-genome, consisting of both cultured and uncultured organisms (metagenomic samples). More recently, the term metagenomic has come to describe a specific type of analysis that relies on high-throughput nucleic-acid sequencing of either 16S rDNA or whole-community DNA (metagenomic sequencing). This chapter will examine studies using both metagenomic samples, and the use of metagenomic sequencing to gather information on functional genes that code for antibiotic resistance. Although the focus here will be on mining metagenomic data for information on antibiotic resistance genes, it is acknowledged that functional gene-based metagenomic studies complement experiments involving gene expression, protein production, and phenotypic characterization of individual and community resistance.

Last Modified: 8/21/2014
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